The top career official at Japan’s health ministry called the scandal over flawed studies of a Novartis AG drug a “big shock” and said the ministry would take action after receiving a report expected soon from a ministry study body.

“We have received a big shock over this affair,” Atsuko Muraki, vice minister of health, labor and welfare, said in an interview in Washington. “It has caused worries and a lack of trust … in the process by which new drugs are developed.”

“Those who were using the drug also were probably confused and worried” by the reports of altered data, Ms. Muraki said.

Novartis has apologized for carrying out promotions that cited the flawed research but denied involvement in any distortion of the clinical data.

A health ministry study group led by Nagoya University emeritus law professor Akio Morishima has been looking into the matter. It is expected to report its initial conclusions by the end of September, Ms. Muraki said, adding that the ministry would use the results to determine what kind of action is needed to prevent a recurrence of the scandal.

Novartis spokesman Eric Althoff said the company is cooperating fully with the study group. “Novartis is committed to cooperating with the health ministry and supports the intentions of the health ministry to further review investigator initiated trials in Japan to establish guidance and practices to ensure credibility of research in Japan,” Mr. Althoff said by e-mail.

One aspect the panel is looking into is the marketing and promotional activities carried out by Novartis using Diovan studies that were based on flawed data.

Ms. Muraki said it was possible that other agencies would look into taking action against Novartis, naming the education ministry and “the world of criminal justice” as parts of the government that might take a look at the company’s actions.

She observed that prosecutors enjoy powers of investigation and interrogation that other ministries such as her own do not. However, she said she hadn’t heard anything from prosecutors as to whether they were looking into the case, and she said she didn’t know whether the company did anything illegal. Mr. Althoff said the company is not aware of any criminal investigation by Japanese prosecutors.

The health ministry can take action against the company if it’s found to have violated Japanese pharmaceutical law through excessive or misleading advertising. Companies or individuals found to have violated the rules could face a fine of up to ¥2 million, or a prison sentence of up to two years. The health ministry could also remove a drug maker’s manufacturing and sales license.

Ms. Muraki, who took office in July, is just the second woman to hold the position of administrative vice minister—the top career post–at a Japanese government ministry. The first was a vice minister in the 1990s at what was then known as the Labor Ministry.

About Japan Real Time

Japan Real Time is a newsy, concise guide to what works, what doesn’t and why in the one-time poster child for Asian development, as it struggles to keep pace with faster-growing neighbors while competing with Europe for Michelin-rated restaurants. Drawing on the expertise of The Wall Street Journal and Dow Jones Newswires, the site provides an inside track on business, politics and lifestyle in Japan as it comes to terms with being overtaken by China as the world’s second-biggest economy. You can contact the editors at japanrealtime@wsj.com